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- PDB-3fo8: Crystal structure of the bacteriophage T4 tail sheath protein, pr... -

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Basic information

Entry
Database: PDB / ID: 3fo8
TitleCrystal structure of the bacteriophage T4 tail sheath protein, protease resistant fragment gp18PR
ComponentsTail sheath protein Gp18
KeywordsVIRAL PROTEIN / mostly beta / viral structural protein / bacteriophage T4 / tail sheath
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2160 / Thrombin, subunit H - #380 / : / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / : / Tail sheath protein, subtilisin-like domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2160 / Thrombin, subunit H - #380 / : / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tail sheath protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsAksyuk, A.A. / Leiman, P.G. / Kurochkina, L.P. / Shneider, M.M. / Kostyuchenko, V.A. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: EMBO J / Year: 2009
Title: The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria.
Authors: Anastasia A Aksyuk / Petr G Leiman / Lidia P Kurochkina / Mikhail M Shneider / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less ...The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less than half of its initial length. The sheath consists of 138 copies of the tail sheath protein, gene product (gp) 18, which surrounds the central non-contractile tail tube. The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. A crystal structure of about three quarters of gp18 has been determined and was fitted into cryo-electron microscopy reconstructions of the tail sheath before and after contraction. It was shown that during contraction, gp18 subunits slide over each other with no apparent change in their structure.
History
DepositionDec 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Tail sheath protein Gp18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9462
Polymers29,8871
Non-polymers591
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tail sheath protein Gp18
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)718,71548
Polymers717,29824
Non-polymers1,41724
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_664-x+1,z+1,y-11
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation57_464y-1/2,z+1,x-1/21
crystal symmetry operation58_665-y+3/2,z+1,-x+1/21
crystal symmetry operation59_465y-1/2,-z+1,-x+1/21
crystal symmetry operation60_664-y+3/2,-z+1,x-1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_574z+1/2,-y+2,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_575-z+1/2,-y+2,-x+1/21
crystal symmetry operation77_554z+1/2,x+1/2,y-11
crystal symmetry operation78_566z+1/2,-x+3/2,-y+11
crystal symmetry operation79_564-z+1/2,-x+3/2,y-11
crystal symmetry operation80_556-z+1/2,x+1/2,-y+11
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_665-y+3/2,-x+3/2,-z1
crystal symmetry operation87_465y-1/2,-x+3/2,z1
crystal symmetry operation88_655-y+3/2,x+1/2,z1
Buried area48210 Å2
ΔGint-279.2 kcal/mol
Surface area273280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.665, 203.665, 203.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11D-453-

HOH

21D-707-

HOH

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Components

#1: Protein Tail sheath protein Gp18


Mass: 29887.404 Da / Num. of mol.: 1
Fragment: protease resistant fragment gp18PR: UNP Residues 83-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 18, GB AAA32541.1 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13332
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE COMPLETELY AGREES WITH THE GENBANK ENTRY AAA32541, PUBMED REPORT ...AUTHORS STATE THAT THE SEQUENCE COMPLETELY AGREES WITH THE GENBANK ENTRY AAA32541, PUBMED REPORT 2964531. THE SEQUENCE DIFFERENCES MAY REFLECT THE SEQUENCE VARIATION BETWEEN THE VIRUS STRAINS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2M Sodium acetate, 1M Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942, 0.97956, 0.97818
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979561
30.978181
ReflectionResolution: 1.8→36 Å / Num. obs: 61873 / % possible obs: 88.11 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.064 / Χ2: 2.867 / Net I/σ(I): 26.802
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2 / Num. unique all: 2112 / Χ2: 1.19 / % possible all: 95.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→36 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.835 / SU ML: 0.22 / σ(F): 1.88 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflection
Rfree0.219 2785 4.99 %
Rwork0.19 --
all0.2141 61873 -
obs0.191 55815 88.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.779 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 63.35 Å2 / Biso mean: 22.108 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 8 422 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052110
X-RAY DIFFRACTIONf_angle_d1.0132870
X-RAY DIFFRACTIONf_chiral_restr0.073330
X-RAY DIFFRACTIONf_plane_restr0.005373
X-RAY DIFFRACTIONf_dihedral_angle_d15.563746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.2661320.2592539267185
1.83-1.8640.2771360.242607274387
1.864-1.90.2951180.2462597271586
1.9-1.9380.3271260.2322607273386
1.938-1.980.2541300.2242609273986
1.98-2.0260.2761340.2152565269986
2.026-2.0770.2151640.2092536270085
2.077-2.1330.2861280.2062503263183
2.133-2.1960.2461610.2062482264384
2.196-2.2670.2751230.2232585270884
2.267-2.3480.231050.2222497260283
2.348-2.4420.281060.2222563266984
2.442-2.5530.2591390.2062547268686
2.553-2.6880.241560.2032642279888
2.688-2.8560.2281340.1992721285590
2.856-3.0760.1941490.1922796294593
3.076-3.3860.1841360.1732876301295
3.386-3.8750.1731620.142901306396
3.875-4.880.1591680.1352908307697
4.88-36.010.1761780.1622949312798

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